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      A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora

      research-article
      Author(s): 1 , 2 , ∗ , 1
      Publication date (Electronic):
      Journal: iScience
      Publisher: Elsevier
      Keywords: Genetics, Evolutionary Biology, Bioinformatics, Omics

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          Summary

          Whole-genome duplication (WGD) has been recognized as a significant evolutionary force in the origin and diversification of multiple organisms. Acropora, a speciose reef-building coral genus, is suspected to have originated by polyploidy. Yet, there is no genetic evidence to support this hypothesis. Using comprehensive phylogenomic and comparative genomic approaches, we analyzed six Acroporid genomes and found that a WGD event likely occurred ∼31 million years ago in the most recent common ancestor of Acropora, concurrent with a worldwide coral extinction. We found that duplicated genes were highly enriched in gene regulation functions, including those of stress responses. The functional clusters of duplicated genes are related to the divergence of gene expression patterns during development. Some proteinaceous toxins were generated by WGD in Acropora compared with other cnidarian species. Collectively, this study provides evidence for an ancient WGD event in corals, which helps explain the origin and diversification of Acropora.

          Graphical Abstract

          Highlights

          • •

            An ancient genome duplication occurred in the most recent common ancestor of Acropora

          • •

            This WGD event likely occurred between 28 and 36 mya in Acropora

          • •

            The WGD event potentially contributes to the origin and diversification of Acropora

          • •

            Duplications of toxic proteins were found in Acropora following the WGD

          Abstract

          Genetics; Evolutionary Biology; Bioinformatics; Omics

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          Whole-genome duplication in teleost fishes and its evolutionary consequences.

          Stella M K Glasauer, Stephan Neuhauss (2014)
          Whole-genome duplication (WGD) events have shaped the history of many evolutionary lineages. One such duplication has been implicated in the evolution of teleost fishes, by far the most species-rich vertebrate clade. After initial controversy, there is now solid evidence that such event took place in the common ancestor of all extant teleosts. It is termed teleost-specific (TS) WGD. After WGD, duplicate genes have different fates. The most likely outcome is non-functionalization of one duplicate gene due to the lack of selective constraint on preserving both. Mechanisms that act on preservation of duplicates are subfunctionalization (partitioning of ancestral gene functions on the duplicates), neofunctionalization (assigning a novel function to one of the duplicates) and dosage selection (preserving genes to maintain dosage balance between interconnected components). Since the frequency of these mechanisms is influenced by the genes' properties, there are over-retained classes of genes, such as highly expressed ones and genes involved in neural function. The consequences of the TS-WGD, especially its impact on the massive radiation of teleosts, have been matter of controversial debate. It is evident that gene duplications are crucial for generating complexity and that WGDs provide large amounts of raw material for evolutionary adaptation and innovation. However, it is less clear whether the TS-WGD is directly linked to the evolutionary success of teleosts and their radiation. Recent studies let us conclude that TS-WGD has been important in generating teleost complexity, but that more recent ecological adaptations only marginally related to TS-WGD might have even contributed more to diversification. It is likely, however, that TS-WGD provided teleosts with diversification potential that can become effective much later, such as during phases of environmental change.
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            Polyploidy and genome evolution in plants.

            Pamela Soltis, D Blaine Marchant, Yves Van de Peer … (2015)
            Plant genomes vary in size and complexity, fueled in part by processes of whole-genome duplication (WGD; polyploidy) and subsequent genome evolution. Despite repeated episodes of WGD throughout the evolutionary history of angiosperms in particular, the genomes are not uniformly large, and even plants with very small genomes carry the signatures of ancient duplication events. The processes governing the evolution of plant genomes following these ancient events are largely unknown. Here, we consider mechanisms of diploidization, evidence of genome reorganization in recently formed polyploid species, and macroevolutionary patterns of WGD in plant genomes and propose that the ongoing genomic changes observed in recent polyploids may illustrate the diploidization processes that result in ancient signatures of WGD over geological timescales.
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              Balancing biodiversity in a changing environment: extinction debt, immigration credit and species turnover.

              Stephen Jackson, Dov Sax (2010)
              Here, we outline a conceptual framework for biodiversity dynamics following environmental change. The model incorporates lags in extinction and immigration, which lead to extinction debt and immigration credit, respectively. Collectively, these concepts enable a balanced consideration of changes in biodiversity following climate change, habitat fragmentation and other forcing events. They also reveal transient phenomena, such as biodiversity surpluses and deficits, which have important ramifications for biological conservation and the preservation of ecosystem services. Predicting such transient dynamics poses a serious conservation challenge in a time of rapid environmental change.
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                Author and article information

                Contributors
                Yafei Mao
                Journal
                Journal ID (nlm-ta): iScience
                Journal ID (iso-abbrev): iScience
                Title: iScience
                Publisher: Elsevier
                ISSN (Electronic): 2589-0042
                Publication date PMC-release: 06 February 2019
                Publication date Collection: 29 March 2019
                Publication date (Electronic): 06 February 2019
                Volume: 13
                Pages: 20-32
                Affiliations
                [1 ]Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
                Author notes
                [∗ ]Corresponding author yafei.mao@ 123456oist.jp
                [2]

                Lead Contact

                Article
                Publisher ID: S2589-0042(19)30035-5
                DOI: 10.1016/j.isci.2019.02.001
                PMC ID: 6389592
                PubMed ID: 30798090
                SO-VID: 837297c1-7b51-4684-bffb-69bbf12bace2
                Copyright © © 2019 The Author(s)
                License:

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                Date received : 10 July 2018
                Date revision received : 28 January 2019
                Date accepted : 31 January 2019
                Categories
                Subject: Article

                Keywords: genetics,evolutionary biology,bioinformatics,omics
                Data availability:
                Keywords: genetics, evolutionary biology, bioinformatics, omics

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